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 ### CCP4 7.0.078: Refmac          version 5.8.0258 : 09/10/19##
 ###############################################################
 User: maly  Run date: 26/ 5/2020 Run time: 13:30:53 


 Please reference: Collaborative Computational Project, Number 4. 2011.
 "Overview of the CCP4 suite and current developments". Acta Cryst. D67, 235-242.
 as well as any specific reference in the program write-up.


 $TEXT:Reference1: $$ Primary reference $$ 
   "Overview of refinement procedures within REFMAC5: utilizing data from different sources"
   O.Kovalevskiy, R.A.Nicholls, F.Long, G.N.Murshudov,(2018) 
   Acta Crystallogr. D74, 492-505

 $$
 $SUMMARY :Reference1:  $$ Refmac: $$
 :TEXT:Reference1: $$

 $TEXT:Reference1: $$ Primary reference for EM $$ 
   "Current approaches for the fitting and refinement of atomic models into cryo-EM maps using CCP-EM
   R.A. Nicholls, M. Tykac, O.Kovalevskiy, G.N.Murshudov,(2018) 
   Acta Crystallogr. D74, 215-227

 $$
 $SUMMARY :Reference2:  $$ Refmac: $$
 :TEXT:Reference1: $$

 $TEXT:Reference1: $$ Secondary reference $$ 
   "REFMAC5 for the refinement of macromolecular crystal structures:"
   G.N.Murshudov, P.Skubak, A.A.Lebedev, N.S.Pannu, R.A.Steiner, R.A.Nicholls, M.D.Winn, F.Long and A.A.Vagin,(2011) 
   Acta Crystallogr. D67, 355-367

 $$
 $SUMMARY :Reference3:  $$ Refmac: $$
 :TEXT:Reference1: $$

 $TEXT:Reference2: $$ Secondary reference $$ 
   "Refinement of Macromolecular Structures by the  Maximum-Likelihood Method:"
   G.N. Murshudov, A.A.Vagin and E.J.Dodson,(1997)
   Acta Crystallogr. D53, 240-255
   EU  Validation contract: BIO2CT-92-0524

 $$
 $SUMMARY :Reference4:  $$ Refmac: $$
 :TEXT:Reference2: $$

  Data line--- make     check NONE
  Data line--- refi     type REST reso 41.96 1.92     resi MLKF     meth CGMAT     bref MIXED
  Data line--- scal     type SIMP     LSSC     ANISO     EXPE
  Data line--- solvent YES
  Data line--- bins 4
  Data line--- ncyc 10
  Data line--- monitor MEDIum
  Data line--- free 0
  Data line--- END

 OPENED INPUT MTZ FILE 
 Logical Name: HKLIN   Filename: CDO_R.mtz 

 LABIN FP=FP SIGFP=SIGFP FREE=FreeR_flag

    ****                     Input and Default parameters#                      ****


Input coordinate file.  Logical name - XYZIN actual file name  - CDO_step0-01A_R00_1-93A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_step0-01A_R00_1-92A.pdb
Input reflection file.  Logical name - HKLIN actual file name  - CDO_R.mtz
Output reflection file. Logical name - HKLOUT actual file name - CDO_step0-01A_R00_1-92A.mtz

Cell from mtz :    57.632    57.632   122.391    90.000    90.000    90.000
Space group from mtz: number -   96; name - P 43 21 2

  Refinement type                        : Restrained

    ****                           Makecif parameters                           ****

Dictionary files for restraints : /protein2/ccp4/ccp4-7.0/ccp4-7.0/lib/data/monomers/mon*cif
Parameters for new entry and VDW: /protein2/ccp4/ccp4-7.0/ccp4-7.0/lib/data/monomers/ener_lib.cif
    Program will rely on residue and atom names. No checking
    If this option is used then monomers should be checked carefully before using
    Hydrogens will be restored in their riding positions
    Links between monomers will be checked. Only those links present in the coordinate file will be used
    Standard sugar links will be analysed and used
    For new ligands "ideal restraint" values will be taken from the energetic libary ener_lib.cif
    Symmetry related links will be analysed and used
    Cis peptides will be found and used automatically


  Residual                               : Rice Maximum Likelihood for Fs

    ****                    Least-square scaling parameters                     ****

Overall scale
Overall B value
Overall anisotropic B with tr(B) = 0.0
Constant bulk solvent in non protein region
Probe radii for non-ions     1.200
Probe radii for ions         0.800
Shrinkage of the mask  by    0.800


    ****                 Map sharpening parameters and methods                  ****

No map sharpening will be performed

  Method of minimisation                 : Sparse Matrix
  Experimental sigmas used for weighting
  Number of Bins and width:     4       0.0678
  Refinement of mixed isotropic and anisotropic Bfactors
  Refinement resln        :    41.9635  1.9200
  Estimated number of reflections :      21526
  Free R exclusion - flag equals:     0
  Auto weighting. An attempt
  Refinement cycles       :    10
  Scaling type                           :
          Wilson scaling type with Guassians

  Estimation of D/Sigma in resolution bins
  using  free set of reflns with experimental sigmas
  using  free set of reflns with experimental sigmas

  Scaling and SigmaA resln:    41.9635  1.9200

  Damping factors:     1.0000  1.0000  1.0000


    ****                    Geometry restraints and weights                     ****


                                              Sigma:
 Bonding distances
          Weight =  1.00

 Bond angles
          Weight =  1.00

 Planar groups (all and main chain)
          WEIGHT= 1.00 1.00

 Chiral centers
          Weight= 1.00

 NON-BONDED CONTACTS
          Overall weight                          =  1.00
          Sigma for simple VDW                    =  0.20
          Sigma for VDW trhough torsion angle     =  0.20
          Sigma for HBOND                         =  0.20
          Sigma for metal-ion                     =  0.20
          Sigma for DUMMY and other atom          =  0.30
          Distance for donor-accepetor = vdw1+vdw2+(-0.30)
          Distance for acceptor - H    = vdw1+     ( 0.10)
          VDW distance through torsion = vdw1+vdw2+(-0.30)
          Distance for DUMMY-others    = vdw1+vdw2+(-0.70)

 TORSION ANGLES
          Weight= 1.00

 THERMAL FACTORS
          Weight= 1.00
     Main chain bond (1-2 neighbour)          1.5A**2
     Main chain angle (1-3 neighbour)         2.0A**2
     Side chain bond                          3.0A**2
     Side chain angle                         4.5A**2

 RESTRAINTS AGAINST EXCESSIVE SHIFTS
     Positional parameters                   0.00A
     Thermal parameters                      0.00A
     Occupancy parameters                    0.00

 RADIUS OF CONFIDENCE
     Positional parameters 0.00A
     Thermal parameters    0.00A**2
     Occupancy parameters  0.00

Monitoring style is "MEDIUM". Complete information will be printed out in the
first and last cycle. In all other cycles minimum information will be printed out
Sigma cutoffs for printing out outliers
If deviation of restraint parameter > alpha*sigma then information will be printed out
Distance outliers      10.000
Angle outliers         10.000
Torsion outliers       10.000
Chiral volume outliers 10.000
Plane outliers         10.000
Non-bonding outliers   10.000
B value  outliers      10.000
Rigid bond outliers    10.000
Sphericity outliers    10.000
---------------------------------------------------------------

 Input file :CDO_step0-01A_R00_1-93A.pdb
  ------------------------------
  ---  LIBRARY OF MONOMERS   ---
 _lib_name         mon_lib
 _lib_version      5.51
 _lib_update       11/07/18
  ------------------------------
  NUMBER OF MONOMERS IN THE LIBRARY          : 24624
                with complete description    : 24624
  NUMBER OF MODIFICATIONS                    :    70
  NUMBER OF LINKS                            :    77
  I am reading libraries. Please wait.
      - energy parameters
      - monomer"s description (links & mod )
  Number of atoms    :    1836
  Number of residues :     502
  Number of chains   :       4
  I am reading library. Please wait.
                mon_lib.cif
  INFO:     link is found (not be used) dist=   1.991 ideal_dist=   2.090
            ch:AAA  res:  86  HIS              at:NE2 .->ch:AaA  res: 501  FE               at:FE  .
  INFO:     link is found (not be used) dist=   2.201 ideal_dist=   2.090
            ch:AAA  res:  88  HIS              at:NE2 .->ch:AaA  res: 501  FE               at:FE  .
  INFO:     link is found (not be used) dist=   1.843 ideal_dist=   1.720
            ch:AAA  res:  93  CYS              at:SG  .->ch:AAA  res: 157  TYR              at:CE1 .
  INFO:     link is found (not be used) dist=   2.203 ideal_dist=   2.090
            ch:AAA  res: 140  HIS              at:NE2 .->ch:AaA  res: 501  FE               at:FE  .
  INFO:     link is found (not be used) dist=   2.363 ideal_dist=   1.945
            ch:AaA  res: 501  FE               at:FE  .->ch:AbA  res: 901  2CO              at:N   .
  INFO:     link is found (not be used) dist=   2.422 ideal_dist=   2.235
            ch:AaA  res: 501  FE               at:FE  .->ch:AbA  res: 901  2CO              at:SG  .
  INFO:     link is found (not be used) dist=   2.097 ideal_dist=   1.870
            ch:AaA  res: 501  FE               at:FE  .->ch:AbA  res: 901  2CO              at:OD  .
  --------------------------------
  --- title of input coord file ---

  PDB_code:xxxx
  PDB_name:----
  PDB_date:22-OCT-19
  --------------------------------
  ATTENTION: atom:OXT  PRO               190  AAA  is missing in the structure
  Number of chains                  :       4
  Total number of monomers          :     502
  Number of atoms                   :    3945
  Number of missing atoms           :       1
  Number of rebuilt atoms           :    1480
  Number of unknown atoms           :       0
  Number of deleted atoms           :       0

_ccp4_form_factor.scat_method    'Sum of Gaussians'
_ccp4_form_factor.scat_data_source  X-ray


 loop_
     _atom_type_symbol
     _atom_type_scat_Cromer_Mann_a1
     _atom_type_scat_Cromer_Mann_b1
     _atom_type_scat_Cromer_Mann_a2
     _atom_type_scat_Cromer_Mann_b2
     _atom_type_scat_Cromer_Mann_a3
     _atom_type_scat_Cromer_Mann_b3
     _atom_type_scat_Cromer_Mann_a4
     _atom_type_scat_Cromer_Mann_b4
     _atom_type_scat_Cromer_Mann_c


  N     12.2220   0.0057   3.1346   9.8933   2.0141  28.9975   1.1672   0.5826 -11.5379
  H      0.4930  10.5109   0.3229  26.1257   0.1402   3.1424   0.0408  57.7997   0.0030
  C      2.3103  20.8439   1.0201  10.2075   1.5888   0.5687   0.8651  51.6512   0.2156
  O      3.0487  13.2771   2.2870   5.7011   1.5464   0.3239   0.8671  32.9089   0.2508
  S      6.9054   1.4679   5.2035  22.2151   1.4379   0.2536   1.5863  56.1720   1.0490
  FE    11.7738   4.7611   7.3600   0.3072   3.5235  15.3535   2.3054  76.8805   1.2805


 Number of distances         :           0
 Number of angles            :           0
 Number of torsions          :           0
 Number of planes            :           0
 Number of chirals           :           0
 Number of intervals         :           0
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
                        Standard  External       All
                Bonds:      2949         0      2949
               Angles:      5344         0      5344
              Chirals:       196         0       196
               Planes:       453         0       453
             Torsions:      1556         0      1556
            Intervals:         0         0         0
--------------------------------------------------------------------------------


  Number of harmonic restraints       =            0
  Number of atoms in special position =            0
 -----------------------------------------------------


    ****                           Info from mtz file                           ****

FreeR flag                            0
Number of "free" reflections        840
Number of   all  reflections      16472
--------------------------------------------------------------------------------
 Number of reflections in file      39842
 Number of reflections read          16472

   Current auto weighting coefficient =    7.2998581    

 mode : HKRF


######  TLS Group Definitions ######



     CGMAT cycle number =      1

    ****                              VDW outliers                              ****

VDW deviations from the ideal >10.000Sigma or dist <  1.000 will be monitored

A     93 CYS SG  . - A    157 TYR HE1 . mod.= 0.910 id.= 3.000 dev= -2.09 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   112  112  240
 Maximuum H,K,L                 :    31   31   64
 Minimum acceptable grid spacing:    72   72  153
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   112  112  240
 Maximuum H,K,L                 :    31   31   64
 Minimum acceptable grid spacing:    72   72  153
 Weight matrix   0.20860913    
 Actual weight    7.2998581      is applied to the X-ray term
Norm of X_ray positional gradient                30.9
Norm of Geom. positional gradient                77.5
Norm of X_ray B-factor gradient                  107.
Norm of Geom. B-factor gradient                  105.
Product of X_ray and Geom posit. gradients     -0.867E+07
 Cosine of angle between them                      -0.374
Product of X_ray and Geom B-fact gradients     -0.334E+08
 Cosine of angle between them                      -0.926


Residuals: XRAY=     0.6248E+06 GEOM=     0.1260E+05 TOTAL=     0.6374E+06
 function value    637436.56    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.011     0.013
Bond distances: others                         1391     0.035     0.017
Bond angles  : refined atoms                   2106     1.697     1.644
Bond angles  : others                          3238     2.344     1.580
Torsion angles, period  1. refined              185     7.038     5.000
Torsion angles, period  2. refined               90    36.841    22.778
Torsion angles, period  3. refined              268    14.269    15.000
Torsion angles, period  4. refined                9    11.111    15.000
Chiral centres: refined atoms                   196     0.084     0.200
Planar groups: refined atoms                   1743     0.010     0.020
Planar groups: others                           332     0.016     0.020
VDW repulsions: refined_atoms                   305     0.242     0.200
VDW repulsions.others                          1331     0.221     0.200
VDW; torsion: refined_atoms                     715     0.170     0.200
VDW; torsion.others                             711     0.079     0.200
HBOND: refined_atoms                            231     0.206     0.200
Metal-ion: refined_atoms                          1     0.009     0.200
VDW repulsions: symmetry: refined_atoms          10     0.205     0.200
VDW repulsions: symmetry: others                 25     0.196     0.200
HBOND: symmetry: refined_atoms                   21     0.211     0.200
M. chain bond B values: refined atoms           746     1.520     1.204
M. chain bond B values: others                  746     1.519     1.204
M. chain angle B values: refined atoms          929     2.455     1.792
M. chain angle B values: others                 930     2.454     1.792
S. chain bond B values: refined atoms           811     2.433     1.528
S. chain bond B values: others                  810     2.430     1.528
S. chain angle B values: refined atoms         1177     3.853     2.150
S. chain angle B values: others                1178     3.851     2.150
Long range B values: refined atoms             1859     6.596    16.817
Long range B values: others                    1757     6.288    15.425
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0401, B  =   -0.0890
Partial structure    1: scale =     0.3753, B  =   46.4879
Overall anisotropic scale factors
   B11 =  -0.27 B22 =  -0.27 B33 =   0.54 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------

    ****                Things for loggraph, R factor and others                ****


$TABLE: Cycle    1. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle    1.  v. resln :N:1,6,7,11,12:
:Cycle    1.  and  v. resln :N:1,4,5,9,10:
:Cycle    1. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.034    2154 100.00   483.3   487.1  0.16  0.17      96   478.1   486.2  0.20  0.22
 0.102    3608 100.00   394.4   376.4  0.16  0.15     181   391.3   365.6  0.22  0.21
 0.170    4533  99.96   251.0   247.3  0.16  0.13     266   271.0   260.1  0.21  0.19
 0.237    5332 100.00   195.3   195.0  0.16  0.13     297   199.1   200.0  0.23  0.19
$$

    ****                      Fom and SigmaA vs resolution                      ****

 $TABLE: Cycle    1. FSC and  Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle    1. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0344   1480   0.908    674   0.806   2154   0.876  0.959  0.9608  0.9686  0.9140  0.9424
  0.1021   2928   0.879    680   0.762   3608   0.857  0.997  0.9438  0.9614  0.8747  0.9442
  0.1698   3856   0.863    677   0.773   4533   0.849  0.974  0.9462  0.9564  0.8925  0.9389
  0.2374   4649   0.864    686   0.740   5335   0.848  0.959  0.9395  0.9559  0.8602  0.9391
 $$
Resolution limits                    =     41.964     1.920
Number of used reflections           =      15630
Percentage observed                  =    99.9818
Percentage of free reflections       =     5.1002
Overall R factor                     =     0.1593
Free R factor                        =     0.2170
Average Fourier shell correlation    =     0.9590
AverageFree Fourier shell correlation=     0.9450
Overall weighted R factor            =     0.1493
Free weighted R factor               =     0.2019
Overall weighted R2 factor           =     0.1816
Free weighted R2 factor              =     0.2439
Average correlation coefficient      =     0.9407
Overall correlation coefficient      =     0.9550
Free correlation coefficient         =     0.9109
Cruickshanks DPI for coordinate error=     0.1465
DPI based on free R factor           =     0.1453
Overall figure of merit              =     0.8543
ML based su of positional parameters =     0.0907
ML based su of thermal parameters    =     3.0347
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    85596.242       12596.102       637436.56      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.21436712    
 Actual weight    7.2998581      is applied to the X-ray term


 function value    631720.25    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.011     0.013
Bond distances: others                         1391     0.002     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0400, B  =   -0.1299
Partial structure    1: scale =     0.3751, B  =   46.5595
Overall anisotropic scale factors
   B11 =  -0.27 B22 =  -0.27 B33 =   0.54 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1593
Free R factor                        =     0.2164
Average Fourier shell correlation    =     0.9600
AverageFree Fourier shell correlation=     0.9460
Average correlation coefficient      =     0.9410
Overall figure of merit              =     0.8576
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    85429.422       8097.5459       631720.25       637436.56    


     CGMAT cycle number =      3

 Weight matrix   0.21439117    
 Actual weight    7.2998581      is applied to the X-ray term


 function value    631651.00    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.011     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0400, B  =   -0.1332
Partial structure    1: scale =     0.3752, B  =   46.4092
Overall anisotropic scale factors
   B11 =  -0.27 B22 =  -0.27 B33 =   0.54 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1590
Free R factor                        =     0.2165
Average Fourier shell correlation    =     0.9601
AverageFree Fourier shell correlation=     0.9460
Average correlation coefficient      =     0.9412
Overall figure of merit              =     0.8577
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    85417.109       8118.2813       631651.00       631720.25    


     CGMAT cycle number =      4

 Weight matrix   0.21425958    
 Actual weight    7.2998581      is applied to the X-ray term


 function value    631623.00    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.011     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0400, B  =   -0.1346
Partial structure    1: scale =     0.3752, B  =   46.2919
Overall anisotropic scale factors
   B11 =  -0.27 B22 =  -0.27 B33 =   0.54 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1590
Free R factor                        =     0.2165
Average Fourier shell correlation    =     0.9601
AverageFree Fourier shell correlation=     0.9460
Average correlation coefficient      =     0.9412
Overall figure of merit              =     0.8577
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    85412.672       8122.6499       631623.00       631651.00    


     CGMAT cycle number =      5

 Weight matrix   0.21420066    
 Actual weight    7.2998581      is applied to the X-ray term


 function value    631587.13    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.011     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0400, B  =   -0.1394
Partial structure    1: scale =     0.3751, B  =   46.0904
Overall anisotropic scale factors
   B11 =  -0.27 B22 =  -0.27 B33 =   0.54 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1590
Free R factor                        =     0.2166
Average Fourier shell correlation    =     0.9601
AverageFree Fourier shell correlation=     0.9460
Average correlation coefficient      =     0.9412
Overall figure of merit              =     0.8577
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    85408.359       8118.2559       631587.13       631623.00    


     CGMAT cycle number =      6

 Weight matrix   0.21409571    
 Actual weight    7.2998581      is applied to the X-ray term


 function value    631569.25    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.011     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0400, B  =   -0.1444
Partial structure    1: scale =     0.3751, B  =   46.1191
Overall anisotropic scale factors
   B11 =  -0.27 B22 =  -0.27 B33 =   0.54 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1590
Free R factor                        =     0.2166
Average Fourier shell correlation    =     0.9601
AverageFree Fourier shell correlation=     0.9460
Average correlation coefficient      =     0.9412
Overall figure of merit              =     0.8576
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03
 fvalues    85406.578       8113.3574       631569.25       631587.13    


     CGMAT cycle number =      7

 Weight matrix   0.21369655    
 Actual weight    7.2998581      is applied to the X-ray term


 function value    631589.38    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.011     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0400, B  =   -0.1487
Partial structure    1: scale =     0.3751, B  =   46.0535
Overall anisotropic scale factors
   B11 =  -0.27 B22 =  -0.27 B33 =   0.54 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1590
Free R factor                        =     0.2166
Average Fourier shell correlation    =     0.9601
AverageFree Fourier shell correlation=     0.9459
Average correlation coefficient      =     0.9412
Overall figure of merit              =     0.8575
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05


 fvalues    85410.516       8105.9277       631600.88       631569.25    

 fvalues    85410.516       8105.9277       631581.06       631590.56    
 fvalues    85410.516       8105.9277       631581.06       631590.56    


     CGMAT cycle number =      8

 Weight matrix   0.21345684    
 Actual weight    7.2998581      is applied to the X-ray term


 function value    631604.44    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.011     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0400, B  =   -0.1507
Partial structure    1: scale =     0.3751, B  =   46.1083
Overall anisotropic scale factors
   B11 =  -0.27 B22 =  -0.27 B33 =   0.54 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1590
Free R factor                        =     0.2166
Average Fourier shell correlation    =     0.9600
AverageFree Fourier shell correlation=     0.9459
Average correlation coefficient      =     0.9412
Overall figure of merit              =     0.8574
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02

 fvalues    85411.109       8098.7412       631587.75       631590.56    


     CGMAT cycle number =      9

 Weight matrix   0.21342310    
 Actual weight    7.2998581      is applied to the X-ray term


 function value    631598.69    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.011     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0400, B  =   -0.1446
Partial structure    1: scale =     0.3751, B  =   46.1796
Overall anisotropic scale factors
   B11 =  -0.27 B22 =  -0.27 B33 =   0.54 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1590
Free R factor                        =     0.2166
Average Fourier shell correlation    =     0.9600
AverageFree Fourier shell correlation=     0.9459
Average correlation coefficient      =     0.9412
Overall figure of merit              =     0.8574
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02


 fvalues    85412.797       8098.7866       631593.13       631587.75    
 fvalues    85412.797       8098.7866       631593.13       631600.13    


     CGMAT cycle number =     10

    ****                              VDW outliers                              ****

VDW deviations from the ideal >10.000Sigma or dist <  1.000 will be monitored

A     93 CYS SG  . - A    157 TYR HE1 . mod.= 0.936 id.= 3.000 dev= -2.06 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   112  112  240
 Maximuum H,K,L                 :    31   31   64
 Minimum acceptable grid spacing:    72   72  153
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   112  112  240
 Maximuum H,K,L                 :    31   31   64
 Minimum acceptable grid spacing:    72   72  153
 Weight matrix   0.21346709    
 Actual weight    7.2998581      is applied to the X-ray term
Norm of X_ray positional gradient                30.8
Norm of Geom. positional gradient                30.8
Norm of X_ray B-factor gradient                  104.
Norm of Geom. B-factor gradient                  109.
Product of X_ray and Geom posit. gradients     -0.916E+07
 Cosine of angle between them                      -1.000
Product of X_ray and Geom B-fact gradients     -0.357E+08
 Cosine of angle between them                      -0.978


Residuals: XRAY=     0.6235E+06 GEOM=      8097.     TOTAL=     0.6316E+06
 function value    631585.63    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.011     0.013
Bond distances: others                         1391     0.001     0.017
Bond angles  : refined atoms                   2106     1.703     1.644
Bond angles  : others                          3238     1.419     1.580
Torsion angles, period  1. refined              185     7.022     5.000
Torsion angles, period  2. refined               90    36.768    22.778
Torsion angles, period  3. refined              268    14.348    15.000
Torsion angles, period  4. refined                9    11.475    15.000
Chiral centres: refined atoms                   196     0.084     0.200
Planar groups: refined atoms                   1743     0.009     0.020
Planar groups: others                           332     0.001     0.020
VDW repulsions: refined_atoms                   302     0.242     0.200
VDW repulsions.others                          1368     0.192     0.200
VDW; torsion: refined_atoms                     711     0.170     0.200
VDW; torsion.others                             780     0.083     0.200
HBOND: refined_atoms                            230     0.206     0.200
Metal-ion: refined_atoms                          1     0.003     0.200
VDW repulsions: symmetry: refined_atoms           9     0.214     0.200
VDW repulsions: symmetry: others                 25     0.187     0.200
HBOND: symmetry: refined_atoms                   21     0.210     0.200
M. chain bond B values: refined atoms           746     1.525     1.209
M. chain bond B values: others                  746     1.524     1.209
M. chain angle B values: refined atoms          929     2.466     1.799
M. chain angle B values: others                 930     2.464     1.798
S. chain bond B values: refined atoms           811     2.440     1.536
S. chain bond B values: others                  810     2.437     1.535
S. chain angle B values: refined atoms         1177     3.865     2.160
S. chain angle B values: others                1178     3.863     2.160
Long range B values: refined atoms             1853     6.530    16.888
Long range B values: others                    1751     6.191    15.450
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0400, B  =   -0.1446
Partial structure    1: scale =     0.3752, B  =   46.1644
Overall anisotropic scale factors
   B11 =  -0.27 B22 =  -0.27 B33 =   0.54 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------

    ****                Things for loggraph, R factor and others                ****


$TABLE: Cycle   10. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle   10.  v. resln :N:1,6,7,11,12:
:Cycle   10.  and  v. resln :N:1,4,5,9,10:
:Cycle   10. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.034    2154 100.00   483.6   487.5  0.16  0.17      96   478.4   486.8  0.20  0.22
 0.102    3608 100.00   394.6   376.6  0.16  0.15     181   391.5   366.3  0.22  0.20
 0.170    4533  99.96   251.2   247.3  0.16  0.13     266   271.1   259.8  0.21  0.19
 0.237    5332 100.00   195.4   195.2  0.16  0.13     297   199.2   200.3  0.23  0.19
$$

    ****                      Fom and SigmaA vs resolution                      ****

 $TABLE: Cycle   10. FSC and  Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle   10. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0344   1480   0.920    674   0.820   2154   0.889  0.959  0.9634  0.9712  0.9134  0.9423
  0.1021   2928   0.883    680   0.768   3608   0.862  0.997  0.9459  0.9628  0.8775  0.9443
  0.1698   3856   0.862    677   0.773   4533   0.849  0.974  0.9464  0.9565  0.8936  0.9396
  0.2374   4649   0.865    686   0.741   5335   0.849  0.959  0.9398  0.9567  0.8589  0.9401
 $$
Resolution limits                    =     41.964     1.920
Number of used reflections           =      15630
Percentage observed                  =    99.9818
Percentage of free reflections       =     5.1002
Overall R factor                     =     0.1590
Free R factor                        =     0.2166
Average Fourier shell correlation    =     0.9601
AverageFree Fourier shell correlation=     0.9459
Overall weighted R factor            =     0.1492
Free weighted R factor               =     0.2014
Overall weighted R2 factor           =     0.1817
Free weighted R2 factor              =     0.2434
Average correlation coefficient      =     0.9412
Overall correlation coefficient      =     0.9552
Free correlation coefficient         =     0.9116
Cruickshanks DPI for coordinate error=     0.1462
DPI based on free R factor           =     0.1450
Overall figure of merit              =     0.8575
ML based su of positional parameters =     0.0895
ML based su of thermal parameters    =     3.0097
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02
 fvalues    85411.094       8096.7202       631585.63       631600.13    

    ****                              VDW outliers                              ****

VDW deviations from the ideal >10.000Sigma or dist <  1.000 will be monitored

A     93 CYS SG  . - A    157 TYR HE1 . mod.= 0.936 id.= 3.000 dev= -2.06 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 LABOUT FreeR_flag=FreeR_flag FP=FP SIGFP=SIGFP FC=FC PHIC=PHIC FC_ALL=FC_ALL PHIC_ALL=PHIC_ALL FWT=FWT PHWT=PHWT DELFWT=DELFWT PHDELWT=PHDELWT FOM=FOM FC_ALL_LS=FC_ALL_LS PHIC_ALL_LS=PHIC_ALL_LS

 WRITTEN OUTPUT MTZ FILE 
 Logical Name: HKLOUT   Filename: CDO_step0-01A_R00_1-92A.mtz 




-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.011     0.013
Bond distances: others                         1391     0.001     0.017
Bond angles  : refined atoms                   2106     1.703     1.644
Bond angles  : others                          3238     1.419     1.580
Torsion angles, period  1. refined              185     7.021     5.000
Torsion angles, period  2. refined               90    36.767    22.778
Torsion angles, period  3. refined              268    14.361    15.000
Torsion angles, period  4. refined                9    11.483    15.000
Chiral centres: refined atoms                   196     0.084     0.200
Planar groups: refined atoms                   1743     0.009     0.020
Planar groups: others                           332     0.001     0.020
VDW repulsions: refined_atoms                   302     0.242     0.200
VDW repulsions.others                          1369     0.192     0.200
VDW; torsion: refined_atoms                     712     0.170     0.200
VDW; torsion.others                             784     0.083     0.200
HBOND: refined_atoms                            230     0.206     0.200
Metal-ion: refined_atoms                          1     0.003     0.200
VDW repulsions: symmetry: refined_atoms           9     0.214     0.200
VDW repulsions: symmetry: others                 25     0.187     0.200
HBOND: symmetry: refined_atoms                   21     0.210     0.200
M. chain bond B values: refined atoms           746     1.525     1.209
M. chain bond B values: others                  746     1.524     1.209
M. chain angle B values: refined atoms          929     2.466     1.799
M. chain angle B values: others                 930     2.465     1.799
S. chain bond B values: refined atoms           811     2.440     1.536
S. chain bond B values: others                  810     2.437     1.536
S. chain angle B values: refined atoms         1177     3.864     2.161
S. chain angle B values: others                1178     3.862     2.160
Long range B values: refined atoms             1853     6.530    16.891
Long range B values: others                    1751     6.191    15.453
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0400, B  =   -0.1490
Partial structure    1: scale =     0.3753, B  =   46.1895
Overall anisotropic scale factors
   B11 =  -0.27 B22 =  -0.27 B33 =   0.54 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------

    ****                Things for loggraph, R factor and others                ****


$TABLE: Cycle   11. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle   11.  v. resln :N:1,6,7,11,12:
:Cycle   11.  and  v. resln :N:1,4,5,9,10:
:Cycle   11. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.034    2154 100.00   483.7   487.5  0.16  0.17      96   478.5   486.9  0.20  0.22
 0.102    3608 100.00   394.7   376.6  0.16  0.15     181   391.6   366.4  0.22  0.20
 0.170    4533  99.96   251.2   247.3  0.16  0.13     266   271.2   259.8  0.21  0.19
 0.237    5332 100.00   195.4   195.2  0.16  0.13     297   199.3   200.3  0.23  0.19
$$

    ****                      Fom and SigmaA vs resolution                      ****

 $TABLE: Cycle   11. FSC and  Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle   11. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0344   1480   0.921    674   0.820   2154   0.889  0.959  0.9634  0.9712  0.9133  0.9422
  0.1021   2928   0.883    680   0.768   3608   0.862  0.997  0.9460  0.9628  0.8777  0.9443
  0.1698   3856   0.862    677   0.773   4533   0.849  0.974  0.9464  0.9565  0.8936  0.9396
  0.2374   4649   0.865    686   0.740   5335   0.849  0.959  0.9398  0.9567  0.8588  0.9401
 $$
Resolution limits                    =     41.964     1.920
Number of used reflections           =      15630
Percentage observed                  =    99.9818
Percentage of free reflections       =     5.1002
Overall R factor                     =     0.1590
Free R factor                        =     0.2165
Average Fourier shell correlation    =     0.9601
AverageFree Fourier shell correlation=     0.9459
Overall weighted R factor            =     0.1492
Free weighted R factor               =     0.2013
Overall weighted R2 factor           =     0.1816
Free weighted R2 factor              =     0.2432
Average correlation coefficient      =     0.9412
Overall correlation coefficient      =     0.9552
Free correlation coefficient         =     0.9116
Cruickshanks DPI for coordinate error=     0.1462
DPI based on free R factor           =     0.1450
Overall figure of merit              =     0.8575
ML based su of positional parameters =     0.0895
ML based su of thermal parameters    =     3.0097
-----------------------------------------------------------------------------
  Time in seconds: CPU =        14.62
             Elapsed =           0.00

    ****           Things for loggraph, R factor and others vs cycle            ****


$TABLE: Rfactor analysis, stats vs cycle  :
$GRAPHS: vs cycle :N:1,2,3:
:FOM vs cycle :N:1,4:
:-LL vs cycle :N:1,5:
:-LLfree vs cycle :N:1,6:
:Geometry vs cycle:N:1,7,8,9,10,11:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.1593   0.2170   0.854       85596.    4764.4   0.0111  0.822   1.697  0.987   0.084
       1   0.1593   0.2164   0.858       85429.    4762.5   0.0108  0.798   1.682  0.978   0.084
       2   0.1590   0.2165   0.858       85417.    4762.6   0.0110  0.816   1.694  0.985   0.084
       3   0.1590   0.2165   0.858       85413.    4762.6   0.0110  0.816   1.698  0.987   0.084
       4   0.1590   0.2166   0.858       85408.    4762.4   0.0110  0.816   1.700  0.988   0.084
       5   0.1590   0.2166   0.858       85407.    4762.5   0.0110  0.817   1.701  0.988   0.084
       6   0.1590   0.2166   0.858       85410.    4763.0   0.0110  0.816   1.702  0.989   0.084
       7   0.1590   0.2166   0.857       85413.    4763.2   0.0110  0.816   1.702  0.989   0.084
       8   0.1590   0.2166   0.857       85413.    4763.2   0.0110  0.816   1.703  0.989   0.084
       9   0.1590   0.2166   0.857       85411.    4763.2   0.0110  0.815   1.703  0.989   0.084
      10   0.1590   0.2165   0.857       85413.    4763.3   0.0110  0.815   1.703  0.989   0.084
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.1593   0.1590
             R free    0.2170   0.2165
     Rms BondLength    0.0111   0.0110
      Rms BondAngle    1.6971   1.7033
     Rms ChirVolume    0.0839   0.0836
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      45.7s System:    0.1s Elapsed:     0:46